I have data that contains some real experimental values and -999.00 (no data available for that time) and I want to interpolate across the "missing" data. However, the user may not want to interpolate across the entire time frame that the data is displayed for. So I thought I would lay it out like this:

% t is time and x is the corresponding data
% Plot the data so the user can see it, red if it is a missing data point, blue otherwise:

figure
hold on
for i=1:length(x)
if x(i)==-999.00
plot(t(i),0,'r^')
else
plot(t(i),x(i),'bo')
end
end
hold off

% Get starting values for interpolation
[t1,x1]=ginput(1);

% Interpolate over necessary sections using t1,x1 as the first data point.

The only problem with using ginput is it grabs the value of the user's click, and not the closest plotted data point to the user's click. Is there a way of getting [t1,x1] to be the values of the closest data point?

% Get difference between the t array and where they clicked.
diffs = abs(t - t1);
% Find out where that difference is minimum.
[minDiff, indexAtMin] = min(diffs);
% Now we know the index (the element number)
% so find the value of t at that index.
tClosestToUserClick = t(indexAtMin);

I'm assuming you know how to interpolate just the -999 points, right (since you didn't ask about that specifically)?